Generalities

All code associated to this page can be found here (https://github.com/svalbuenaa/UlcerativeColitisBulkRNAseq)

Raw counts matrix

Obtaining metadata information

Patient IDs

157
877
1057
1077
1192
1214
8854
8855
8874
8878
8879
8881

Area from which samples were obtained

Ascending
Descending
Large
Rectum
Sigmoid
Tranverse

Lognormalization of counts

Most variable genes

Mean vs CoV for all genes

Mean vs CoV for most variable genes

Principal component analysis (PCA)

PCA with all genes

Scree plot

PCA Scores

PCA with 500 most variable genes

PCA Scores

Differential expression analysis

GO enrichment up and down-regulated genes

Heatmap top 50 DEGs

Based on p.adj

Z-score norm

Plot single genes

standardGeneric for "plot" defined from package "base"

function (x, y, ...) 
standardGeneric("plot")
<environment: 0x00000262c22b8860>
Methods may be defined for arguments: x, y
Use  showMethods(plot)  for currently available ones.